cellrank: Cell trajectories with 'CellRank'

In trichelab/velocessor: The world's dumbest single-cell RNA velocity calculator and loader

Description

Use RNA velocity to find root or final states via the CellRank package. Most of this is a straight-up ripoff of velociraptor so that I can learn how to operate Python via basilisk for CellRank and SignatureFinder-GPU to run.

Usage

cellrank(x, ...)

## S4 method for signature 'SingleCellExperiment'
cellrank(x, ...)

Arguments

x	The output of velociraptor::scvelo().

Details

This function uses the CellRank Python package (which can be found at https://pypi.org/project/cellrank/) for RNA velocity-pseudotime informed root and leaf finding when constructing trajectories and the like. This is done via the basilisk package - see the documentation for that package for trouble-shooting.

Value

A SingleCellExperiment is returned containing the output.

Author(s)

Tim Triche, Jr.

Examples

# Using mock data to demonstrate the process:
library(scuttle)
sce1 <- mockSCE()
sce2 <- mockSCE()

spliced <- counts(sce1)
unspliced <- counts(sce2)

mats <- list(X=spliced, spliced=spliced, unspliced=unspliced)
velo <- velociraptor::scvelo(mats)
cellrank <- cellrank(velo)

trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.